CS-327-1: Computational Methods in Biology
College of Arts & Sciences Syllabus
Spring 2019

COURSE INFORMATION
Credit Hours:
3.0
Course Description:
Bioinformatics is the discipline that applies mathematics, statistics, computer science, chemistry, and biology to solving problems in biology using biological data sets. The problems investigated are usually at the molecular level. These problems include sequence alignment, genome assembly, models of evolution and phylogenetic trees, analyzing gene expression data, and gene linkage analysis. One of the most important statistical tools used in bioinformatics is the Bayesian network. This course introduces the techniques used in bioinformatics, in particular Bayesian networks, and provides solutions to several bioinformatics problems.
Prerequisites:
CS-201 or MATH-251 (A grade of C or higher is required), BIO-100 or BIO-201 (A grade of C or higher is required), CS-200 (A grade of C or higher is required)
Class Time:
Monday/Wednesday 4:15 p.m. - 5:30 p.m.
Class Location:
Lech Walesa Hall 2054
FACULTY INFORMATION
Instructor:
Rachel Trana
Office Location:
Lech Walesa Hall 3049
Office Hours:
Monday 5:45 p.m. - 6:45 p.m.
Wednesday 5:45 p.m. - 6:45 p.m.
Thursday 1:00 p.m. - 3:00 p.m.
Phone Extension:
773.442.4723
Email:
r-trana@neiu.edu
Per university policy, grades may not be discussed via email.
All course-related questions should be posted on the D2L Discussion Forum.
COURSE MATERIALS
Required Text:
Bioinformatics Algorithms An Active Learning Approach, 3rd Edition, ISBN: 978-0-9903746-3-3
Additional Resources:
As this is an interdisciplinary course, materials will be taken from a variety of sources. Students can also reference the additional resources below.

Introduction to Bioinformatics Algorithms, Neil C. Jones and Pavel A. Pevzner, MIT Press, 2004. ISBN-13: 978-0262101066

A Molecular Biology Primer, Phillip Compeau

A Primer on Molecular Biology, Alexander Zien

An Introduction to Python
http://tdc-www.harvard.edu/Python.pdf http://greenteapress.com/thinkpython/html/index.html https://www.stat.berkeley.edu/~spector/pythonslides.pdf
Websites:
  • Grades, Homework Submissions (some assignments): D2L
  • Discussion Forum: Piazza
  • Course Lectures, Study Guides, Homework Assignments, Schedule: racheltrana/CS327_1.html
  • Additional homework assignments: Rosalind
COURSE OBJECTIVES / STUDENT LEARNING OUTCOMES
Upon completing CS-327: Computational Methods in Biology, students will be able to:
  • Apply computer science principles to solving problems in biology.
  • Investigate some of the algorithmic ideas, such as dynamic programming and graph theory, that are fundamental to an understanding of modern biology.
  • Prepare students to work in the interdisciplinary area of recent advances in high-performance computing and biology, especially with the massive information resources of the human genome.
  • Increase computational literacy.
  • Understand the principles and some methods of genomics, gene expression and proteomics that aid precision medicine, modern plant and animal breeding.
  • Work with large, complicated datasets that once took researchers years to manually analyze.
MAJOR TOPICS
  • Introduction to Molecular Biology
  • Introduction to Python
  • Genome Replication: Transcription, Translation
  • Sequencing Antibiotics
  • Genome Alignment
  • Genomic Data: Genome databases
  • Genome Rearrangements
STUDENT TASKS / ASSIGNMENTS / REQUIREMENTS
Attendance:
Attendance is mandatory. More than six (6) absences will result in an automatic F in the course.
Assignments:
Homework will be assigned weekly, posted online. While working on homework assignments with other students is encouraged, plagiarism is NOT tolerated. All work should be unique. Students that submit duplicate/identical work will receive an F for that homework assignment. All assignments must be submitted to D2L by the specified due date and time. There are NO exceptions.
Quizzes:
There will be several online (D2L) quizzes throughout the semester, designed to reinforce core concepts in Programming II. These quizzes must be completed by the specified due date and time (no extensions will be given).
Requirements for Graduate Students:
In addition to completing homework assignments and taking the midterm and final exams, graduate students will be given a specific project topic within the field of computational biology in which they will need to research and implement biological algorithm. All work must be unique. Students that plagiarize on their project will receive an F for the course. This will be graded as pass/fail. Graduate students that fail the project will drop a full letter grade when calculating their final grade.
Grading Policies and Formulae:
Item Weight
Homework 15%
Quizzes 10%
Midterm 37.5%
Final Exam 37.5%
Percentage Letter Grade
90 - 100 % A
80 - 89.99999999 % B
70 - 79.99999999 % C
60 - 69.99999999 % D
0 - 59.99999999 % F
Exams:
There will be a midterm exam, worth 37.5% of your final grade and a final exam, also worth 37.5% of your final grade. The final exam date isWednesday, May 1 from 4:00 - 5:50 p.m. This is set by the university final exam schedule, which is posted online. There are NO make-up exams. The material in this course builds on itself and therefore the material for the exams is implicitly cumulative. Exams are closed-book and closed-notes. Access to any digital devices is prohibited.
UNIVERSITY POLICIES AND STATEMENTS
Academic Integrity Policy:
By enrolling in this course, you are bound by the NEIU Student Code of Conduct. You will be informed by your instructor of any additional policy specific to your course regarding plagiarism, class disruptions, etc.
ADA Statement:
Northeastern Illinois University (NEIU) complies with the Americans with Disabilities Act (ADA) in making reasonable accommodations for qualified students with disabilities. To request accommodations, students with special needs should make arrangements with the Student Disability Services (SDS) office, located on the main campus in room D104. Contact SDS via (773) 442-4595 or http://www.neiu.edu/university-life/student-disability-services. It is your responsibility to have the Accessibility Center send me this information by the 3rd week of the semester.
Campus Safety:
Web links to Campus Safety: Emergency Procedures and Safety Information can be found on NEIUport on the MyNEIU tab or as follows: http://homepages.neiu.edu/~neiutemp/Emergency_Procedures/MainCampus/.
COURSE POLICIES AND STATEMENTS
Absence Policy:
Attendance is mandatory. More than six (6) absences will result in an automatic F in the course.
Submitting Assignments to D2L:
  1. Create a folder with your name and in that folder include all of your homework files (program code, input and output files, but NO .class files).
  2. Compress the folder. For Windows: Right-click and choose “Send to” and then choose "Compressed (zipped) Folder".
  3. Submit the zipped folder (.zip file) to D2L Dropbox.
General Policies:
  • No grade of "I" will be given.
  • No makeup exams or quizzes will be given. If you miss an exam or quiz, you will receive an F for that exam/quiz.
  • You must bring your NEIU ID to each exam, including the final exam. I reserve the right to check your ID at each exam, including the final exam.
  • The use of cell phones, iPads or computers during class time for non-class or non-emergency purposes is not allowed. Phones are to be muted and laptops/iPads are to remain closed.
  • There will be NO extra credit projects given to improve grades.
  • Cheating and/or plagiarism will not be tolerated. Students that violate the NEIU academic conduct policy may be subject to an F for that assignment, quiz, exam, project or any portion (or all) of the final course grade
  • Policies may be modified or added as I deem appropriate/necessary.
Important Dates:
Monday, January 21, 2019: Martin Luther King, Jr. Birthday (No Classes)
Tuesday, February 12, 2019: Lincoln’s Birthday (No Classes)
Monday, March 18 - Sunday, March 24, 2019: Spring Break (No Classes)
Friday, March 29, 2019: Last day to drop with a W